Entamoeba histolytica vs Pythium ultimum Translated Blat Results

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Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Entamoeba histolytica was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 1,589

Genome coverage (bp) Coding exon coverage (bp)
Entamoeba histolytica

Uncovered: 20,528,838 out of 20,835,395
Covered: 306,557 out of 20,835,395

Uncovered: 9,950,019 out of 10,244,611
Matches: 177,610 out of 10,244,611
Mismatches: 116,954 out of 10,244,611
Insertions: 28 out of 10,244,611

Pythium ultimum DAOM BR144

Uncovered: 44,727,034 out of 44,913,582
Covered: 186,548 out of 44,913,582

Uncovered: 19,651,163 out of 19,826,256
Matches: 104,846 out of 19,826,256
Mismatches: 70,214 out of 19,826,256
Insertions: 33 out of 19,826,256

Configuration parameters

ParameterValue
Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

Entamoeba histolytica Pythium ultimum
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}